A method is presented for obtaining accurate positron emission tomography transmission measurements after tracer injection. A transmission scan is performed using a rotating source immediately before or after a conventional emission scan. Sinogram windowing, which removes most scattered and random coincidences, also removes most of the emission counts contaminating the transmission measurement. Data from the emission scan can be used to subtract the remaining emission counts to produce accurate transmission measurements. For studies with moderate to low emission count rates (e.g., fluorodeoxyglucose) there is little increase in noise in the resulting attenuation correction factors. This method was tested in experiments with phantoms and a rotating source simulator and validated against conventional ring transmission measurements. Applications of the technique can significantly shorten the time between transmission and emission studies, and thereby reduce the likelihood of patient motion and increase scanning throughput.